Update geo_tools.c

sPuReMD/src/geo_tools.c

@@ -487,8 +487,13 @@ void Read_BGF( const char * const bgf_file, reax_system* system, control_params
     char element[6], charge[9];
     char chain_id;
     char s_a[12], s_b[12], s_c[12], s_alpha[12], s_beta[12], s_gamma[12];
-    char *endptr = NULL;
-    int i, atom_cnt, token_cnt, bgf_serial, ratom = 0;
+    char *endptr;
+    int i, atom_cnt, token_cnt, bgf_serial, ratom, crystx_found;
+
+    endptr = NULL;
+    ratom = 0;
+    crystx_found = FALSE;
+
 
     /* open biograf file */
     bgf = sfopen( bgf_file, "r" );
@@ -512,8 +517,9 @@ void Read_BGF( const char * const bgf_file, reax_system* system, control_params
         tokens[0][0] = 0;
         token_cnt = Tokenize( line, &tokens, MAX_TOKEN_LEN );
 
-        if ( !strncmp( tokens[0], "ATOM", MAX_TOKEN_LEN )
-                || !strncmp( tokens[0], "HETATM", MAX_TOKEN_LEN ) )
+        if ( !strncmp( tokens[0], "ATOM", 4 )
+                || !strncmp( tokens[0], "HETATM", 6 ) )
+
         {
             ++system->N;
         }
@@ -665,6 +671,8 @@ void Read_BGF( const char * const bgf_file, reax_system* system, control_params
             Setup_Box( atof(s_a), atof(s_b), atof(s_c),
                     atof(s_alpha), atof(s_beta), atof(s_gamma),
                     &system->box );
+            crystx_found = TRUE;
+
         }
         else if ( !strncmp( tokens[0], "CONECT", 6 ) )
         {
@@ -707,6 +715,21 @@ void Read_BGF( const char * const bgf_file, reax_system* system, control_params
         fprintf( stderr, "[ERROR] Unable to read BGF file. Terminating...\n" );
         exit( INVALID_INPUT );
     }
+    
+    if ( crystx_found == FALSE )
+    {
+        fprintf( stderr, "[ERROR] improperly formatted BGF file (no CRYSTX keyword found). Terminating...\n" );
+        exit( INVALID_INPUT );
+    }
+
+    sfree( line, "Read_BGF::line" );
+    sfree( backup, "Read_BGF::backup" );
+    for ( i = 0; i < MAX_TOKENS; i++ )
+    {
+        sfree( tokens[i], "Read_BGF::tokens[i]" );
+    }
+    sfree( tokens, "Read_BGF::tokens" );
+
 
     sfclose( bgf, "Read_BGF::bgf" );
 }
@@ -741,8 +764,13 @@ void Read_BGF_from_string( char * bgf_str, reax_system* system, control_params *
     char element[6], charge[9];
     char chain_id;
     char s_a[12], s_b[12], s_c[12], s_alpha[12], s_beta[12], s_gamma[12];
-    char *endptr = NULL;
-    int i, atom_cnt, token_cnt, bgf_serial, ratom = 0;
+    char *endptr;
+    int i, atom_cnt, token_cnt, bgf_serial, ratom, crystx_found;
+
+    endptr = NULL;
+    ratom = 0;
+    crystx_found = FALSE;
+
 
 
     /* allocate memory for tokenizing biograf file lines */
@@ -764,8 +792,9 @@ void Read_BGF_from_string( char * bgf_str, reax_system* system, control_params *
         tokens[0][0] = 0;
         token_cnt = Tokenize( line, &tokens, MAX_TOKEN_LEN );
 
-        if ( !strncmp( tokens[0], "ATOM", MAX_TOKEN_LEN )
-                || !strncmp( tokens[0], "HETATM", MAX_TOKEN_LEN ) )
+        if ( !strncmp( tokens[0], "ATOM", 4 )
+                || !strncmp( tokens[0], "HETATM", 6 ) )
+
         {
             ++system->N;
         }
@@ -919,6 +948,8 @@ void Read_BGF_from_string( char * bgf_str, reax_system* system, control_params *
             Setup_Box( atof(s_a), atof(s_b), atof(s_c),
                     atof(s_alpha), atof(s_beta), atof(s_gamma),
                     &system->box );
+                    
+            crystx_found = TRUE;
         }
         else if ( !strncmp( tokens[0], "CONECT", 6 ) )
         {
@@ -956,6 +987,21 @@ void Read_BGF_from_string( char * bgf_str, reax_system* system, control_params *
             tokens[i][0] = 0;
         }
     }
+    
+    if ( crystx_found == FALSE )
+    {
+        fprintf( stderr, "[ERROR] improperly formatted BGF file (no CRYSTX keyword found). Terminating...\n" );
+        exit( INVALID_INPUT );
+    }
+
+    sfree( line, "Read_BGF::line" );
+    sfree( backup, "Read_BGF::backup" );
+    for ( i = 0; i < MAX_TOKENS; i++ )
+    {
+        sfree( tokens[i], "Read_BGF::tokens[i]" );
+    }
+    sfree( tokens, "Read_BGF::tokens" );
+
     /*
     if ( ferror( bgf ) )
     {